global: smaller fixes of Cookiecutter template

[lnielsen]

• Remove pypi and coverage badge in README (readme: delete coverage and pypi badge #107).
• Update readme to use v3.1 instead of v3.0 in the example (readme: adapt to version 3.1 installation #108).
• Update readme with documentation of all new parameters(readme: add new parameters #109).
• Link directly to https://inveniosoftware.org/#getstarted instead of invenio.readthedocs.io (Fixed indirectly by readme: adapt to version 3.1 installation #108 ?).
• Remove todo to # TODO: Redefine these permissions to cover your auth needs (todos: delete permission factory todo #112 and invenio#3919)
• Fix instance's INSTALL.rst to mention (docs: fix installation.rst #111):
  • How to activate a virtualenv with pipenv shell (ask Lars for where to put it)
  • Change UWSGI -> uWSGI.
• Use the project_site cookiecutter variable whenever a domain is needed. E.g. in config.py (config: change domains to project_site #110):
  • SUPPORT_EMAIL = 'info@{{cookiecutter.project_site}}'
  • APP_ALLOWED_HOSTS = ['{{cookiecutter.project_site}}', 'localhost', '127.0.0.1']